Updated samtools to 0.1.19

[rsem.git] / sam / bedcov.c

diff --git a/sam/bedcov.c b/sam/bedcov.c
new file mode 100644 (file)
index 0000000..3e4b952
--- /dev/null
+++ b/sam/bedcov.c
@@ -0,0 +1,127 @@
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include "kstring.h"
+#include "bgzf.h"
+#include "bam.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+typedef struct {
+       bamFile fp;
+       bam_iter_t iter;
+       int min_mapQ;
+} aux_t;
+
+static int read_bam(void *data, bam1_t *b)
+{
+       aux_t *aux = (aux_t*)data;
+       int ret = bam_iter_read(aux->fp, aux->iter, b);
+       if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+       return ret;
+}
+
+int main_bedcov(int argc, char *argv[])
+{
+       extern void bam_init_header_hash(bam_header_t*);
+       gzFile fp;
+       kstring_t str;
+       kstream_t *ks;
+       bam_index_t **idx;
+       bam_header_t *h = 0;
+       aux_t **aux;
+       int *n_plp, dret, i, n, c, min_mapQ = 0;
+       int64_t *cnt;
+       const bam_pileup1_t **plp;
+
+       while ((c = getopt(argc, argv, "Q:")) >= 0) {
+               switch (c) {
+               case 'Q': min_mapQ = atoi(optarg); break;
+               }
+       }
+       if (optind + 2 > argc) {
+               fprintf(stderr, "Usage: samtools bedcov <in.bed> <in1.bam> [...]\n");
+               return 1;
+       }
+       memset(&str, 0, sizeof(kstring_t));
+       n = argc - optind - 1;
+       aux = calloc(n, sizeof(void*));
+       idx = calloc(n, sizeof(void*));
+       for (i = 0; i < n; ++i) {
+               aux[i] = calloc(1, sizeof(aux_t));
+               aux[i]->min_mapQ = min_mapQ;
+               aux[i]->fp = bam_open(argv[i+optind+1], "r");
+               idx[i] = bam_index_load(argv[i+optind+1]);
+               if (aux[i]->fp == 0 || idx[i] == 0) {
+                       fprintf(stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]);
+                       return 2;
+               }
+               bgzf_set_cache_size(aux[i]->fp, 20);
+               if (i == 0) h = bam_header_read(aux[0]->fp);
+       }
+       bam_init_header_hash(h);
+       cnt = calloc(n, 8);
+
+       fp = gzopen(argv[optind], "rb");
+       ks = ks_init(fp);
+       n_plp = calloc(n, sizeof(int));
+       plp = calloc(n, sizeof(void*));
+       while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
+               char *p, *q;
+               int tid, beg, end, pos;
+               bam_mplp_t mplp;
+
+               for (p = q = str.s; *p && *p != '\t'; ++p);
+               if (*p != '\t') goto bed_error;
+               *p = 0; tid = bam_get_tid(h, q); *p = '\t';
+               if (tid < 0) goto bed_error;
+               for (q = p = p + 1; isdigit(*p); ++p);
+               if (*p != '\t') goto bed_error;
+               *p = 0; beg = atoi(q); *p = '\t';
+               for (q = p = p + 1; isdigit(*p); ++p);
+               if (*p == '\t' || *p == 0) {
+                       int c = *p;
+                       *p = 0; end = atoi(q); *p = c;
+               } else goto bed_error;
+
+               for (i = 0; i < n; ++i) {
+                       if (aux[i]->iter) bam_iter_destroy(aux[i]->iter);
+                       aux[i]->iter = bam_iter_query(idx[i], tid, beg, end);
+               }
+               mplp = bam_mplp_init(n, read_bam, (void**)aux);
+               bam_mplp_set_maxcnt(mplp, 64000);
+               memset(cnt, 0, 8 * n);
+               while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0)
+                       if (pos >= beg && pos < end)
+                               for (i = 0; i < n; ++i) cnt[i] += n_plp[i];
+               for (i = 0; i < n; ++i) {
+                       kputc('\t', &str);
+                       kputl(cnt[i], &str);
+               }
+               puts(str.s);
+               bam_mplp_destroy(mplp);
+               continue;
+
+bed_error:
+               fprintf(stderr, "Errors in BED line '%s'\n", str.s);
+       }
+       free(n_plp); free(plp);
+       ks_destroy(ks);
+       gzclose(fp);
+
+       free(cnt);
+       for (i = 0; i < n; ++i) {
+               if (aux[i]->iter) bam_iter_destroy(aux[i]->iter);
+               bam_index_destroy(idx[i]);
+               bam_close(aux[i]->fp);
+               free(aux[i]);
+       }
+       bam_header_destroy(h);
+       free(aux); free(idx);
+       free(str.s);
+       return 0;
+}